Protein Alpha Helix: Causes and Function

[lha08]

Homework Statement

I'm a little confused as to how exactly a protein folds into an alpha helix...like what causes it exactly to assume that conformation...does it fold spontaneously in water (like i know hydrophobic R groups cause the protein to fold where the hydrophobic groups are faced towards the inside)? or does it like just simply fold randomly into that shape based on its function without the environment playing any role?
thanks

Homework Equations

The Attempt at a Solution

 

[Ygggdrasil]

Alpha helices are stabilized because amino acids in the helix can form hydrogen bonds with their amide groups to amide groups directly above and below them in the helix. However, in aqueous solution, these amide bonds would form hydrogen bonds with water, so forming an alpha helix provides little additional stability for the folded state. Therefore, most of the time, if you take a sequence that forms an alpha helix in a protein, isolate it from the rest of the protein, and determine its structure in water, it generally will not form an alpha helix spontaneously. In a lipid environment, however, the unfolded state will not be able to form hydrogen bonds with the solvent, so folding into an alpha helix does provide significant stabilization. This is one reason why the transmembrane regions of membrane proteins are very often alpha helical.

Therefore, the rest of the protein's structure (i.e. the chemical environment around the alpha helix) plays a big role in stabilizing an alpha helix's structure.

 

[lha08]

Alpha helices are stabilized because amino acids in the helix can form hydrogen bonds with their amide groups to amide groups directly above and below them in the helix. However, in aqueous solution, these amide bonds would form hydrogen bonds with water, so forming an alpha helix provides little additional stability for the folded state. Therefore, most of the time, if you take a sequence that forms an alpha helix in a protein, isolate it from the rest of the protein, and determine its structure in water, it generally will not form an alpha helix spontaneously. In a lipid environment, however, the unfolded state will not be able to form hydrogen bonds with the solvent, so folding into an alpha helix does provide significant stabilization. This is one reason why the transmembrane regions of membrane proteins are very often alpha helical.

Therefore, the rest of the protein's structure (i.e. the chemical environment around the alpha helix) plays a big role in stabilizing an alpha helix's structure.

So if i understood correctly, in an aqueous environment, the protein prefers to make hydrogen bonds with water via the N--H group of the amine (and also the C double bonded O in the carboxyl?) and therefore the more stable conformation is the unfolded protein?

Like since most protein structures want to be in its most stable conformation, you said that in a lipid environment, folding is more likely, but isn't a lipid environment hydrophobic, so the hydrophobic groups of the protein will just orient themselves towards them? maybe I am just overthinking it though...but what if it folds in a lipid environment, what parts of the alpha protein will face the outside and which on the inside...?

 

[Ygggdrasil]

So if i understood correctly, in an aqueous environment, the protein prefers to make hydrogen bonds with water via the N--H group of the amine (and also the C double bonded O in the carboxyl?) and therefore the more stable conformation is the unfolded protein?

Yes. An unfolded conformation will be more stable than a folded conformation for an isolated alpha helix.

Also, a bit of a nomenclature issue, an amine is a nitrogen attached to only sp³ carbons and hydrogens (e.g. CH₃NH₂). An amide is a -(C=O)-N- group, a nitrogen that is bonded to a carbonyl carbon. Both the oxygen in the C=O group and the H of the N-H of the amide participate in hydrogen bonding.

Like since most protein structures want to be in its most stable conformation, you said that in a lipid environment, folding is more likely, but isn't a lipid environment hydrophobic, so the hydrophobic groups of the protein will just orient themselves towards them? maybe I am just overthinking it though...but what if it folds in a lipid environment, what parts of the alpha protein will face the outside and which on the inside...?

Side chains will always point outside of the alpha helix since there is not enough space inside of the helix to accommodate the side chains.

A good example of how the hydrophobic effect drives protein folding and alpha helix formation in aqueous solution is a leucine zipper. A leucine zipper is an alpha helical structure that contains hydrophobic residues along one face of the helix. Here, it is unfavorable to have the hydrophobic side chains solvated in water in the unfolded state. In order to reach a state of lower free energy, the leucine zipper peptides will form alpha helices and dimerize. Here, the hydrophobic residues become buried in the space between the alpha helices.